Phoma
Phoma Sacc., Michelia 2 (6): 4 (1880).
Index Fungorum number: IF 9358; Facesoffungi number: FoF 08229, 2218 morphological species (Species Fungorum 2022), 2 species with molecular data.
Phytopathogenic. Description in vivo: Sexual morph: Unknown. Asexual morph: Pycnidia mostly superficially formed, simple or compound; wall of pseudoparenchymatic texture; simple pycnidia mostly globular, sometimes lenticular or flask-shaped; compound pycnidia generally much larger. Ostioles somewhat protruding, oozing pinkish or yellow-white spore masses. Pycnidiospores hyaline. Description in vitro: Aerial mycelium usually sparse. Pycnidia abundant, simple or compound; wall of pseudoparenchymatic texture; simple pycnidia mostly globular, sometimes lenticular or flask-shaped, compound pycnidia sometimes even larger. Ostioles distinct. Spore mass abundant, completely covering the pycnidia at maturity, usually salmon pink, but sometimes yellow or white. Pycnidiospores hyaline (adapted from Boerema 1964).
Type species: Phoma herbarum Westend.
Notes: Phoma is characterised by globular, sometimes lenticular or flask-shaped pycnidia forming hyaline conidia in vivo and in vitro. Boerema et al. (1997) divided Phoma into nine sections namely Phoma, Heterospora, Macrospora, Paraphoma, Peyronellaea, Phyllostictoides, Pilosa, Plenodomus and Sclerophomella and this identification system has been very helpful in morphological identification. Phylogenetic analyses from several authors have shown that sections suggested by Boerema et al. (1997) are linked to phylogenetically distinct teleomorph genera and the latter are not always monophyletic (Reddy et al. 1998, Torres et al. 2005, De Gruyter et al. 2009). Boerema et al. (2004) mentioned that the classification of Boerema (1997) is artificial, described approximately 50% of the Phoma taxa and reduced several names to synonymy and identified a total of 215 Phoma taxa and eight teleomorph species with an unnamed Phoma asexual morph. Phoma section Phoma, is characterised by the absence of chlamydospores, septate conidia, and pycnidial ornamentation and comprises taxa that could not be placed elsewhere in the genus Phoma. Phoma herbarium has not been connected to any sexual stage so far. Forty Phoma species placed in sections Phoma, Phyllostictoides and Sclerophomella are associated to a sexual stage in Didymella (Boerema et al. 2004). Aveskamp et al. (2009) also showed that characters that are considered to be specific for a certain section are polyphyletic. For example, dictyochlamydospores and setose pycnidia are the morphological characters of Peyronellaea but are also found in Paraphoma. Phoma has been linked to other sexual genera such as Atradidymella (Davey & Currah 2009), Belizeana (Kohlmeyer & Volkmann-Kohlmeyer 1987), Mycosphaerella (Crous et al. 2009), Fenestella (Zhang et al. 2009) but none of these teleomorph-asexual morph relationships is proven by molecular evidence. Only two Phoma taxa of section Macrospora, P. rabiei and P. zeae-maydis linked to “Mycosphaerella” teleomorphs as M. rabiei are formally recognized (De Gruyter 2002). Mycosphaerella is distinct from all known Phoma taxa hence the use of the names above was recommended (De Gruyter et al. 2009). Schoch et al. (2006, 2009b) and Zhang et al. (2009) mentioned that Phoma phylogenetically clusters in the Pleosporales based on a study using multilocus sequence typing. De Gruyter et al. (2009) mentioned that Phoma is highly polyphyletic. In the phylogenetic analysis of Aveskamp et al. (2009), ACT was more effective in resolving the phylogeny of Phoma exigua below species level. de Gruyter et al. (2009, 2010, 2012) excluded several species from Phoma based on molecular phylogenetic studies using SSU and LSU nucleotide sequences. Aveskamp et al. (2010) re-defined Didymellaceae and included phomoid taxa that could not be accommodated to other genera due to the lack of distinguishing characters and synonymized 15 species under Phoma. Aveskamp et al. (2010) used the ITS, tub2 and act A to clarify the phylogeny of dictyochlamydospore-producing Phoma taxa but several internal nodes were unresolved. The use of ITS as fungal barcode locus in Phoma results in low resolution as the locus is conserved and distort species delimitations or generic boundaries (Nilsson et al. 2008, Aveskamp et al. 2010). Aveskamp et al. (2010) used a combination of four loci namely SSU, LSU, ITS and β-tubulin gene of which the latter provided greater resolution at species level. Chen et al. (2015) used a combined analysis incorporating ITS, LSU, tub2 and RPB2 gene and assigned the sexual morph Atradidymella of Phoma herbarum as the type species of Phoma. Phoma is currently a distinct genus in Didymellaceae and is one of the largest genera with around 2218 taxa but only two species have molecular data. Phoma is a complex genus with very high diversity but taxonomic pitfalls and requires a thorough revision. It is challenging to resolve the taxonomy of Phoma but a kick-start can be by comparing several authentic Phoma cultures from herbarium and check whether isolated Phoma-like taxa are similar with the universal Phoma herbarum. Molecular markers available for Phoma are LSU, SSU, ITS, Actin, BTUB and RPB2.
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